An annotated bibliography summarizes notes about papers being read during a research project. It is one of several methods for working with the knowledge gleaned from reading. The classic annotated bibliography limits the annotation to one paragraph.
In contrast, our modern approach makes the annotation as long and detailed as needed for self-study. It is also not limited to prose. It can include graphical objects of various types to accelerate recall of the paper's content.
This modular approach enables the reuse of annotations in the modular annotated bibliographies of related projects. It has the following enhanced features that the classic annotated bibliography lacks:
- No longer restrained by the
annotefield in the BibTeX entry. - Modular annotation for easy reuse in related projects.
- Images
- Tables
- Equations
- Code blocks
- Hyperlinks: internal and external
- Bibliographic entries can be reordered for subgrouping by category.
- Table of contents, hyperlinked to sections
- Index of terms
- Bibliography includes papers cited outside of those listed in the annotated bibliography.
- List of acronyms used
- List of glossary terms used
- List of mathematical notation
Below is a sample after exportng to PDF. Note the image and the text wrapping of the figure.
Org-mode can be considered a thin wrapper around LaTeX that extends it with additional features. LaTeX is the gold standard for typesetting scientific documents.
The modular bibliographic notes are stored in folders at the top level in the home directory.
The global.bib file is stored in ~/Documents.
Adjust the location and copy the examples to these folders.
mkdir ~/glossaries
mkdir ~/abibNotes
mkdir ~/imagesBlaine # RenameEdit the file paths as needed.
Replace ~/6112MooersLabGitHubLabRepos with the path to wherever you downloaded the file.
Takes a project ID as the only argument.
Run from the top level of your writing project directory.
function maborg {
echo "Create a modular annotated bibliography (mab) subfolder and populate with required files with project number in the title."
if [ $# -lt 1 ]; then
echo 1>&2 "$0: not enough arguments"
echo "Usage1: maborg projectIndexNumber"
return 2
elif [ $# -gt 1 ]; then
echo 1>&2 "$0: too many projectIndexNumber"
echo "Usage1: maborg projectIndexNumber"
return 2
fi
projectID="$1"
mkdir mab$1
cp ~/6112MooersLabGitHubLabRepos/modular-annotated-bibliography-bibtex-org-mode/mabib0573.org ./mab$1/.
cp ~/6112MooersLabGitHubLabRepos/modular-annotated-bibliography-bibtex-org-mode/apacannx.bst ./mab$1/.
cp ~/6112MooersLabGitHubLabRepos/modular-annotated-bibliography-bibtex-org-mode/compile.sh ./mab$1/.
}- git clone this project to your software directory
- Copy one of the bash function and paste into your
.bashrcor.zshrcfile. source .bashrc- cd project directory
- maborg to create subfolder
- Create one tex file per reference in the
~/abibNotes folder. Use the supplied examples as templates. Use the cite key from BibTeX as the name of the bibNote file. Use a blank line between paragraphs. Note that text-wrapping figures is more straightforward than text-wrapping tables. Skip text-wrapping if it is too tedious at this time. Add figures, tables, equations, URLs, citekeys, index macros, acronyms, glossary terms, and math notation as you work. - Use the citekey as the argument of a
\bibentrymacro inside a new subsection heading. This will inject the bibliography entry upon export to PDF. The bibentry package has to be installed in your distribution of LaTeX for this work correctly. - You can cluster citations by topic and subtopic. You can lower the heading level to a subsubsection for the bibliographic entry.
- Compile to HTML to enjoy in a web browser. Compile to PDF to edit while traveling or away from the computer.
- Compiles with texlive; no extra packages required.
These functions save time and are great fun to use.
They can be found in the Emacs Lisp package mooerslab-functions.el found here.
You can use straight or use-package to load these functions directly from GitHub.
Fetch a list of cite keys in a Bibtex file and insert the list at the cursor in the current buffer.
;;; get-citekeys-from-bibtex-file
;% used to work with annotated bibliography. Returns a list under the cursor in the current buffer.
(defun ml/get-citekeys-from-bibtex-file ()
"Prompt for a BibTeX filename in the minibuffer, extract citekeys, and insert an alphabetized itemized list into the current buffer at the cursor position."
(interactive)
(let* ((filename (read-file-name "BibTeX file: ")) ;; Prompt for the BibTeX file
(citekeys '())) ;; Initialize an empty list to store citekeys
(if (not (file-exists-p filename))
(message "File does not exist: %s" filename)
;; Process the BibTeX file
(with-temp-buffer
(insert-file-contents filename) ;; Read the contents of the file into the buffer
(goto-char (point-min)) ;; Move to the beginning of the buffer
;; Search for BibTeX entry keys (e.g., @article{citekey, ...)
(while (re-search-forward "@\\w+{\\([^,]+\\)," nil t)
(let ((citekey (match-string 1))) ;; Extract the citekey from the match
(push citekey citekeys))) ;; Add the citekey to the list
;; Sort the citekeys alphabetically
(setq citekeys (sort citekeys #'string<))))
;; Insert the formatted list into the current buffer
(let ((formatted-citekeys
(mapconcat (lambda (key) (concat " " key)) citekeys "\n")))
(insert formatted-citekeys "\n"))))Use the above list of citekeys or new citekeys found during further reading to generate section headings with the cursor, create a corresponding tex file in the ~/abibNotes folder, and open the tex file in a new buffer.
Org-mode can read LaTeX files with the tex file extension.
;;; wrap-citekey-and-create-tex-file
;% Used to convert a citekey into a section heading.
(defun ml/wrap-citekey-and-create-tex-file ()
"Replace the citekey under the cursor with LaTeX-wrapped text, create a corresponding .tex file, and open it in a new buffer."
(interactive)
(let* ((citekey (thing-at-point 'word t)) ;; Get the citekey under the cursor
(tex-file-dir "/Users/blaine/abibNotes/") ;; Directory for the .tex file
(tex-file-path (concat tex-file-dir citekey ".tex")) ;; Full path for the .tex file
(wrapped-text (format "\\subsection*{\\bibentry{%s}}\n\\Addcontentsline{toc}{subsection}{%s}\n\\input{%s}"
citekey citekey tex-file-path))) ;; LaTeX-wrapped text
(if (not citekey)
(message "No citekey found under the cursor.")
(progn
;; Delete the citekey under the cursor
(let ((bounds (bounds-of-thing-at-point 'word)))
(delete-region (car bounds) (cdr bounds)))
;; Insert the wrapped text in its place
(insert wrapped-text)
;; Create the .tex file if it doesn't already exist
(if (file-exists-p tex-file-path)
(message "File %s already exists." tex-file-path)
(with-temp-file tex-file-path
(insert (format "%% This is the .tex file for citekey: %s\n" citekey))))
;; Open the .tex file in a new buffer
(find-file tex-file-path)
(message "Replaced citekey, created .tex file, and opened it: %s" tex-file-path)))))- still kind of alpha but works in Emacs 29 and 30
- Variant for biblatex.
- NIH: R01 CA242845
- NIH: R01 AI088011
- NIH: P30 CA225520 (PI: R. Mannel)
- NIH: P20 GM103640 and P30 GM145423 (PI: A. West)
| Version | Changes | Date |
|---|---|---|
| 0.1 | Initial commit. | 2024 October 24 |
| 0.2 | Customized the bash script to work in the org files. | 2024 December 11 |
| 0.3 | Add convenience functions. | 2024 December 13 |
| 0.4 | Added MIT license. | 2025 January 7 |
| 0.5 | Added link to mooerslab-functions.el. | 2025 February 26 |